Sunbeam Report extension

This is an extension to generate a visual report from outputs from the Sunbeam pipeline.

Installing

As of Sunbeam version 3.0, simply run:

sunbeam extend https://github.com/sunbeam-labs/sbx_report sunbeam/extensions/sbx_report

Prior to version 3.0, you should manually move or clone the extension directory into the sunbeam/extensions/ folder:

git clone https://github.com/sunbeam-labs/sbx_report sunbeam/extensions/sbx_report

All dependencies are handled by Snakemake and conda at runtime with the --use-conda flag.

Running

To generate the report, simply add --use-conda and specify final_report as the target rule:

sunbeam run --configfile=sunbeam_config.yml --use-conda final_report

(--use-conda will tell Snakemake to automatically maintain a separate conda environment from Sunbeam for this extension, to avoid any package conflicts.)

A self-contained HTML file is generated in your specified output folder under 'reports'.

Example

Click here for an example report.